Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes

• DOI: 10.1371/journal.pone.0260714
• Publication Date: 2021-12-02T19:24:21Z
• Authors: Bastien Paré; Marieke Rozendaal; Sacha Morin; Léa Kaufmann; Shawn M. Simpson; Raphaël Poujol; Fatima Mostefai; Jean-Christophe G...; Henry Xing; Miguelle Sanchez; Ariane Yechouron; Ronald Racette; Julie G. Hussin; Guy Wolf; Ivan Pavlov; Martin A. Smith
• Keywords: Pangolin; Lineage (genetic); Pandemic

The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed this hospital. We performed tiled amplicon whole genome nanopore sequencing nasopharyngeal swabs from all SARS-CoV-2 positive samples 31 March to 17 April 2020 2 local hospitals assess viral diversity (unknown the time Quebec) and potential associations with clinical outcomes. report 264 genomes 242 individuals-both staff patients-with associated features outcomes, as well longitudinal technical replicates. Viral lineage assessment identified multiple subclades both hospitals, predominant subclade outbreak, indicative hospital-acquired transmission. Dimensionality reduction two mutations interest, namely Spike protein, that evaded supervised assignment methods-including Pangolin NextClade tools. also certain symptoms (headache, myalgia sore throat) are significantly favorable patient Our findings demonstrate strength unsupervised, data-driven analyses whilst suggesting caution should be used when employing genomic workflows, particularly during early stages pandemic.